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Wednesday, December 14, 2016

Is genetics still metaphysical? Part I. Some general history.

In very broad terms, modern science has had debates about two basic kinds of approaches to understanding the world. To over-simplify, they are the empirical and the theoretical approaches. Some argue that we can know only what we can detect with our sensory systems (and machines to extend them), but we can never know what general causal principles account for those data, or even if such real, true principles exist. Others view science's essential job as not just accumulating collections of data, which are necessarily imperfect, but to use such observations to build a picture of the true, or perfect underlying regularity--the 'laws' of Nature.

In the former case we just have to make measurements and try to show the ways in which comparable situations lead to comparable outcomes. In the latter, we want what we call 'theory', that is, perfect generalizations that tell us how a given situation will turn out, and what the causal reasons are. The standard assumption of the physical sciences is that Nature is, indeed, universally law-like. Variables like the gravitational constant and the speed of light really are universally, precisely constant.

These are age-old differences, often 'just' philosophical, but they're quite important. Comparably important are the still-unanswered question as to whether any phenomena in Nature is irreducibly probabilistic rather than deterministic, or whether probabilistic aspects of Nature really just reflect our imperfect sampling and measurement. This is the important distinction between epistemology--how we know things, and ontology--how things really are. Can we ever tell the difference?

Empiricism is in some ways the easy part. We just go out and make measurements and let them accumulate so we can generalize about them. That's a lot of slogging to get the data, but all you have to do is be systematic and careful. Don't give me airy generalizations, just the facts, please!

In other ways, theory is the easy part. All you have to do is sit in your armchair, as the proverbial denigratory model has it, and make up something that sounds exotic (or even mathematically intricate) and claim you know how Nature 'is'. Data are imperfect, so don't bother me about that! There are long traditions in both kinds of approach, and to a great extent it's only been the past few hundred years in which there has been melding of these two basic approaches.

Often, theory hypothesizes some fundamental objects whose properties and actions can only be seen indirectly, as they are manifest in measurable phenomena. Here there is a delicate boundary between what is essentially 'metaphysical' as opposed to real. Many object to the use of metaphysical concepts and claims as being essentially untestable, and argue that only empiricism is real and should be taken seriously. In the 19th and early 20th centuries, as technology revealed more and more about unseen Nature, things that were not yet seen directly but that could be hypothesized and assigned to things we could measure, we taken as true by some but denigrated as metaphysical by pure empiricists.

These distinctions were never that clear, in my view (even if they provided jobs for philosophers to write about). Empiricism is retrospective but understanding requires some sorts of predictability, which is prospective. If we cannot reliably generalize, if the same conditions don't always lead to the same result, how can the observing the former lead us to the latter? Predictive power is largely what we want out of science, even if it's just to confirm our understanding of Nature's laws.

Until fairly recently, these issues have mainly been housed in the physical sciences, but since Linnaeus' time, but especially after Darwin and Wallace, the issues have applied to biology as well.
In this brief series we'll try to explore whether or how we can think of biology as the result of such universal laws or whether all we can do is make observations and rough causal generations about them. What is the place for strong causal theory in biology, or are empiricism and very general notions of process enough?

An example from the early prime era in modern science is the 'atom'. Matter was conceived as being composed of these unseen particles, that accounted for the weight and properties of chemicals, and whose movement accounted for the weight, temperature, and pressure in gases. Similar kinds of issues related to electromagnetism: what 'was' it?

An important late 19th-early 20th century example had to do with the existence of 'ether' as the medium through which electromagnetic radiation moved. Ether could not be seen or felt but wavelike radiation had to be waves in something, didn't it? Late-century tests failed to find it (e.g., the famous Michelson-Morely experiment). In well-known interchanges at the time, figures like Ernst Mach, Albert Einstein and Max Planck thought about and debated whether there was a 'real' underlying general 'fabric' of Nature or whether specific empirical data simply showed us enough, and trying to delve deeper was dealing in metaphysics. Many felt that was simply not justified--measurement or empiricism was what science could hope for. On the other hand some, like Einstein, were convinced that Nature had a universal, and real underlying reality of which measurements were reflections. He felt that theory, and in this case mathematics, could reveal or even 'intuit' Nature's underlying fabric. An interesting article by Amanda Gefter in Nautilus science magazine deals with some of this history, with useful references.

So what about biology?
Biology had been largely a descriptive or even theological field before it became a modern science. But then came Darwin and his idea of evolution. He viewed natural selection as a kind of Newtonian universal force. Was it a type of explanation fitted simply around the empirical data that had been collected by Naturalists, or did it constitute some form of universal theory of life as Darwin asserted? Selection as a force had to work through some 'medium' or elements of inheritance. His causal elements ('gemmules') were (like Lamarck's before him) entirely invented to 'fit' what was being observed about the evolution of diversity. Indeed, he modeled natural selection itself after intentional agricultural selection because the latter could be demonstrated by human intent, while the former was generally far too slow to observe directly. But there had to be some 'units' of inheritance for it to work, so he essentially invented them out of thin air. Even in the early 20th century, 'genes' (as they became known) were largely hypothesized units for whose physical nature--or even reality--there was only indirect empirical evidence.

Assuming these discrete causal particles could enable the force, natural selection, to work on adaptive change was much like assuming that electromagnetic radiation needed ether to do its job. Since differential reproductive success is observable, one can always define it to be the result of selection and to assume some gene(s) to be responsible. The test for relative success is, after all, only a statistical one with subjective decision-making criteria (like significance level) in empirical data. In that sense, natural selection is a very metaphysical notion because after the fact we can always empirically observe what has succeeded over time, or what functions have evolved, and call that the result of selection. Such an explanation can hardly be falsified. What is the reality of the underlying force, that Darwin likened to gravity? Since it is always dependent on changing local conditions, what sort of a 'law' is it anyway? And if it's basically metaphysical, should we reject it?

Mendelian genetics as metaphysics
If selection is a process, like gravity, it had to work on objects. Because individual organisms are temporary (they all die), the objects in question had to be transmitted from parent to offspring. That transmission was also found, by Mendel's experiment, to be a regular kind of process. Mendel's causative 'elements', that we now call 'genes', appeared in his carefully chosen pea experiments to be transmitted as discrete things. They fit the discretely causative world of the energized new field of atomic chemistry (see my Evolutionary Anthropology article on Mendel), with its idea that a chemical is made up of a particular kind of atom (thought by some to be multiples of hydrogen at the time), and Mendel's statistical tests showed a reasonably good fit to that discrete-unit worldview (indeed accusations that he or his assistants cheated may reflect his acceptance of discrete underlying but unseen and hence metaphysical, elements). But what were these genes? In what serious sense did they exist as things rather than just an imaginary but essentially unconstrained variables conjured up to account for actual observations--of some sorts of inheritance, that of discretely varying traits--whose actual nature was entirely inaccessible?

These questions became very important in the debate about how evolution worked, since evolution required inheritance of favored states. But what Mendelian analysis, the only 'genetic' analysis available at the time, showed was that the causal genes' effects did not change, and they only were shown to fit discretely varying traits, not the quantitative traits of Darwinian evolution. For these reasons even many mainline evolutionary biologists felt that genes, whatever they were, couldn't account for evolution after all. Maybe geneticists were indulging in metaphysics.

This was similar to the situation that engaged Einstein, Ernst Mach, and others about physics, but when it came to biology, the difference between empiricism and metaphysics became, literally, quite lethal! The tragic impact of Profim Lysenko in the Soviet Union was due to a direct rejection by the scientific power structure that he established based on promises of rapid adaptation in plants, for example to the long, frozen Soviet winters, without adaptive 'genes' having to arise by evolution's slow pace. As I summarized in another Ev. Anth article, it was in part the alleged 'metaphysical' nature of 'genes' in the early 20th century that Lysenko used to reject what most of us would call real science, and put in place an agricultural regime that failed, with mortally disastrous consequences. Along the way, Lysenko with Stalin's help purge many skilled Soviet geneticists, leading many of them to tragic ends. The mass starvation of the era of Lysenkoist agriculture in the USSR may in part have been the result of this view of theoretical science (of course, Lysenko had his own theory, which basically didn't work as it was as much wishful thinking as science).

But how wrong was it to think of genes as metaphysical concepts at the time? Mendel had showed inheritance patterns that seemed to behave, statistically, as if they were caused by specific particles. But he knew many if not most traits did not follow the same pattern. Darwin knew of Mendel's work (and he of Darwin's), but neither thought the other's theories were relevant to his own interests.

But in the first part of the 20th century, the great experimental geneticist TH Morgan used Mendelian ideas in careful breeding experiments to locate 'genes' relative to each other on chromosomes. Even he was an empiricist and avowedly didn't really deal with what genes 'were', just how their causal agency was arranged.

Mendel's work also provided a research experimental approach that led via Morgan and others to the discovery of DNA and its protein coding sequences. We call those sequences 'genes' and research has documented what they are and how they work in great detail. In that sense, and despite early vague guesses about their nature, for most of a century one could assert that genes were in fact quite real, not metaphysical, entities at all. Not only that, but genes were the causal basis of biological traits and their evolution!

But things have turned out not to be so simple or straightforward. Our concept of 'the gene' is in rather great flux, in some ways each instance needing its own ad hoc treatment. Is a regulatory element a 'gene', for example, or a modified epigenetic bit of DNA? Is the 'gene' as still often taught in textbooks still in fact largely a metaphysical concept whose stereotypical properties are convenient but not nearly as informative as is the commonly presented view, even in the scientific literature?

Are we still resting on empiricism, invoking genetic and evolutionary theory as a cover but, often without realizing it, fishing for an adequate underlying theory of biological causation, that would correspond to the seamless reality Einstein (and Darwin, for that matter) felt characterized Nature? Is the gene, like Procrustes, being surgically adapted after the fact, to fit our desired tidy definition? Is claiming a theory on which genetic-based predictions can be 'precise' a false if self-comforting claim, as a marketing tool by NIH, when in fact we don't have the kind of true underlying theory of life that Einstein dreamed of for physics and the cosmos?

2 comments:

Thanks for this effort, Ken. Mechanistic explanations in complex systems can be perilous. I'm not a fan of using the term metaphysics, as "unknown variables and interactions" covers it without mystical overtones. I've read part ll, and look forward to part lll.

I used the term metaphysics because it has long been used as a way of denigrating claims about the world. I agree with your version, and that most scientists when invoking the unknown variables and interactions as if they were known, definite, etc. are not trying to be mystical. But it is a valid critique of much of science when it invents specifics too freely. Probably there's no avoiding that in the frontier of any science. In part III I try to suggest that life may not even have the kind of specific particles or universally applicable 'laws' that are the generally assumed basis of much that's going on, or perhaps more correctly, that we're invoking convenient variables, things, and interactions for rather self-serving and pragmatic reasons, when we should know better--even if we don't, yet, know how to know better.

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